sl-shared-assets 1.0.0rc19__py3-none-any.whl → 1.0.0rc21__py3-none-any.whl

sl_shared_assets/suite2p/single_day.py

@@ -1,563 +0,0 @@
-"""This module stores the classes used to configure the single-day (within-session) sl-suite2p pipeline. This is the
-'original' suite2p pipeline used to process brain activity data collected as part of a single continuous recording. It
-is used as the first step of the multi-day brain activity processing pipeline used in the lab. Both single-day
-(original) and multi-day (extended) pipelines are available as part of the Sun lab maintained sl-suite2p package."""
-
-from typing import Any
-from dataclasses import field, asdict, dataclass
-from pathlib import Path
-import numpy as np
-from ataraxis_base_utilities import ensure_directory_exists
-
-from ataraxis_data_structures import YamlConfig
-
-
-@dataclass
-class Main:
-    """Stores global parameters that broadly define the suite2p single-day processing configuration."""
-
-    nplanes: int = 1
-    """The number of imaging planes, stored as a sequence inside each input TIFF file."""
-
-    nchannels: int = 1
-    """The number of imaging channels per imaging plane. Typically, this is either 1 or 2. The algorithm expects images
-    from different channels of the same plane to be saved sequentially (e.g.: plane 1 ch1, plane 1 ch2, plane 2 ch1, 
-    etc.)."""
-
-    functional_chan: int = 1
-    """The channel used for extracting functional ROIs (cells). Note, this parameter uses 1-based indexing, where '1' 
-    means the first channel and '2' means the second channel."""
-
-    tau: float = 0.4
-    """The timescale of the sensor, in seconds, used for computing the deconvolution kernel. The kernel is fixed to 
-    have this decay and is not fit to the data. Note, the default value is optimized for GCaMP6f animals recorded with 
-    the Mesoscope and likely needs to be increased for most other use cases."""
-
-    force_sktiff: bool = True
-    """Determines whether to force the use of scikit-image (tifffile) for reading TIFF files. Generally, it is 
-    recommended to have this enabled as it forces suite2p to use the tifffile library, which is compatible with more 
-    formats than ScanImage tiff reader. In the future, this option may be deprecated in favor of tifffile altogether."""
-
-    fs: float = 10.0014
-    """The sampling rate per plane in Hertz. For instance, if you have a 10-plane recording acquired at 30Hz, then the 
-    sampling rate per plane is 3Hz, so set this to 3."""
-
-    do_bidiphase: bool = False
-    """Determines whether to perform the computation of bidirectional phase offset for misaligned line scanning 
-    experiments (applies to two-photon recordings only)."""
-
-    bidiphase: int = 0
-    """The user-specified bidirectional phase offset for line scanning experiments. If set to any value besides 0, then 
-    this offset is used and applied to all frames in the recording when 'do_bidiphase' is True. If set to 0, then the 
-    suite2p will estimate the bidirectional phase offset automatically from ‘nimg_init’ frames. The computed or 
-    user-defined offset is applied to all frames before the main processing pipeline."""
-
-    bidi_corrected: bool = False
-    """Tracks whether bidirectional phase correction has been applied to the registered dataset. This argument is 
-    generally not meant to be set by the user and is instead written automatically when the algorithm performs 
-    the bidirectional phase offset correction."""
-
-    frames_include: int = -1
-    """Determines the number of frames of the session's movie to process for each plane. If set to 0, the suite2p will 
-    not do any processing. If negative (-1), the suite2p will process all available frames."""
-
-    multiplane_parallel: bool = False
-    """Determines whether to parallelize plane processing for multi-plane data. Note, plane processing contains some 
-    steps that are automatically parallelized to use all available cores and other that are sequential. Due to this 
-    mixture of steps, processing planes in parallel results in noticeably higher processing speeds, but also increases 
-    the memory (RAM) overhead and average CPU core utilization. Generally, it is recommended to enable this option on 
-    machines with sufficient RAM capacity and CPU core pool size."""
-
-    parallel_planes: int = 3
-    """Determines the maximum number of planes to process in parallel when 'multiplane_parallel' is True. Note, due to 
-    some processing steps being automatically parallelized, this parameter mostly controls the overall core utilization 
-    and RAM overhead. Each parallel plane task will at times try to use all available cores. There are diminishing 
-    returns when setting it to very high values. Most machines should have this set to a value between 3 and 9."""
-
-    ignore_flyback: list[int] = field(default_factory=list)
-    """The list of 'flyback' plane indices to ignore when processing the data. Flyback planes typically contain no valid
-    imaging data, so it is common to exclude them from processing."""
-
-
-@dataclass
-class FileIO:
-    """Stores general I/O parameters that specify input data location, format, and working and output directories."""
-
-    fast_disk: str = ""
-    """The path to the root 'working' directory where to store the temporary binary files created during processing. 
-    This field allows optimizing processing on machines with slow storage drives and fast NVME 'work' drives by caching 
-    all data on the fast drive during runtime. Do not modify this field unless your use case specifically benefits 
-    from caching the data on a different drive than the one that stores the raw data. If this field is not modified, 
-    'save_path0' is used to store the temporary files."""
-
-    delete_bin: bool = False
-    """Determines whether to delete the binary file(s) created during the frame registration stage (registered .bin 
-    file). Note, if the data produced by the 'single-day' pipeline is intended to be later processed as part of the 
-    'multi-day' pipeline, this has to be False. The multi-day pipeline reuses the registered binary files to extract 
-    the fluorescence of cells tracked across days."""
-
-    mesoscan: bool = True
-    """Indicates whether the data submitted to the pipeline are ScanImage Mesoscope multi-page TIFFs."""
-
-    bruker: bool = False
-    """Indicates whether the data submitted to the pipeline are single-page BRUKER TIFFs."""
-
-    bruker_bidirectional: bool = False
-    """Indicates whether BRUKER files contain bidirectional multiplane recordings."""
-
-    h5py: list[str] = field(default_factory=list)
-    """The list of paths to h5py (.hdf / .h5) files to use as pipeline inputs, if the input data uses .h5 format. If 
-    provided, these paths overwrite the 'data_path' field."""
-
-    h5py_key: str = "data"
-    """The key used to access the frame data array inside each input file specified by 'h5py' field paths. This should 
-    only be provided if 'h5py' is not set to an empty list."""
-
-    nwb_file: str = ""
-    """The path to the NWB file to use as pipeline input."""
-
-    nwb_driver: str = ""
-    """The location or name of the driver to use for reading the NWB file."""
-
-    nwb_series: str = ""
-    """The name of the TwoPhotonSeries in the NWB file from which to retrieve the data."""
-
-    save_path0: str = ""
-    """The path to the root output directory where the pipeline results should be saved. Note, the pipeline generates 
-    the 'save_folder' under the root directory specified by this argument and output all data to the generated save 
-    folder."""
-
-    save_folder: str = "suite2p"
-    """The name of the folder under which the pipeline results should be stored. If this is not provided, the pipeline 
-    defaults to using 'suite2p' as the save directory, created under the root directory specified by 'save_path0'. Note,
-    if the data produced by the 'single-day' pipeline is intended to be later processed as part of the 'multi-day' 
-    pipeline, do NOT modify this field. The multi-day pipeline expects the save_folder to be 'suite2p' (default)."""
-
-    data_path: list[str] = field(default_factory=list)
-    """The list of paths to the directories where to search for the input TIFF files. This is used during the initial 
-    conversion of the raw data (expected to be .tiff / .tif) to the binary file format used by the suite2p pipeline."""
-
-    look_one_level_down: bool = False
-    """Determines whether to search for TIFF files in the subfolders of the directories provided as 'data_path' field. 
-    If True, the 'subfolders' field has to be set to a valid list of subfolder names to search."""
-
-    subfolders: list[str] = field(default_factory=list)
-    """Stores specific subfolder names to search through for TIFF files. All subfolders must be stored under the 
-    one or more directories specified by 'data_path'."""
-
-    move_bin: bool = False
-    """Determines whether to move the binary file(s) to the save directory after processing, if 'fast_disk' differs 
-    from the 'save_path0'. Note, if using non-default 'save_folder' name, enabling this option will move the binary 
-    files from the temporary 'suite2p' folder to the 'save_folder'. Otherwise, if the save folder and the temporary 
-    folder are both 'suite2p', the binaries are automatically created and stored inside the 'save_folder'."""
-
-
-@dataclass
-class Output:
-    """Stores parameters for aggregating and saving the processing results of each plane as a unified directory or
-    file."""
-
-    save_nwb: bool = False
-    """Determines whether to save the single-session pipeline output as an NWB file."""
-
-    save_mat: bool = False
-    """Determines whether to save the single-session pipeline output as a MATLAB file (e.g., Fall.mat)."""
-
-    combined: bool = True
-    """Determines whether to combine results across planes into a 'combined' folder at the end of processing. If the 
-    results of the single-day pipeline are intended to be later processed as part of the multi-day pipeline, this has 
-    to be True. This option is safe to use even with single-plane data."""
-
-    aspect: float = 0.666666666
-    """The pixel-to-micron ratio (X:Y) used in the GUI to ensure all images are displayed correctly. This field is not 
-    used during headless processing."""
-
-
-@dataclass
-class Registration:
-    """Stores parameters for rigid registration, which is used to correct motion artifacts between frames by
-    counter-shifting the entire frame."""
-
-    do_registration: bool = True
-    """Determines whether to run the non-rigid motion registration."""
-
-    align_by_chan: int = 1
-    """The channel to use for frame alignment (registration). This field uses 1-based indexing, so 1 means 1st channel 
-    and 2 means 2nd channel. If the recording features both a functional and non-functional channels, it is recommended 
-    to use the non-functional channel for this purpose."""
-
-    nimg_init: int = 500
-    """The number of frames to use to compute the reference image. During registration, each frame is registered to the
-    reference image to remove motion artifacts."""
-
-    batch_size: int = 100
-    """The number of frames to register simultaneously in each batch. When processing data on fast (NVME) drives, 
-    increasing this parameter has minimal benefits and results in undue RAM use overhead. Therefore, on fast drives, 
-    keep this number low. On slow drives, increasing this number may result in faster runtime, at the expense of 
-    increased RAM use."""
-
-    maxregshift: float = 0.1
-    """The maximum allowed shift during registration, given as a fraction of the frame size, in pixels
-    (e.g., 0.1 indicates 10%). This determines how much the algorithm is allowed to shift the entire frame to align it 
-    to the reference image."""
-
-    smooth_sigma: float = 1.15
-    """The standard deviation (in pixels) of the Gaussian filter used to smooth the phase correlation between the 
-    reference image and the current frame."""
-
-    smooth_sigma_time: float = 0.0
-    """The standard deviation (in frames) of the Gaussian used to temporally smooth the data before computing 
-    phase correlation."""
-
-    keep_movie_raw: bool = False
-    """Determines whether to keep the binary file of the raw (non-registered) frames. This is desirable when initially 
-    configuring the suite2p parameters, as it allows visually comparing registered frames to non-registered frames in 
-    the GUI. For well-calibrated runtimes, it is advised to have this set to False."""
-
-    two_step_registration: bool = False
-    """Determines whether to perform a two-step registration. This process consists of the initial registration 
-    (first step) followed by refinement (second step) registration. This procedure is helpful when working with low 
-    signal-to-noise data and requires 'keep_movie_raw' to be set to True."""
-
-    reg_tif: bool = False
-    """Determines whether to write the registered binary data to TIFF files, in addition to keeping it as the .bin 
-    (binary) suite2p files."""
-
-    reg_tif_chan2: bool = False
-    """Determines whether to generate TIFF files for the registered channel 2 data, if processed data contains two 
-    channels."""
-
-    th_badframes: float = 1.0
-    """The threshold for excluding poor-quality frames when performing cropping. Primarily, this is used during two-step
-    registration to exclude frames with excessive motion from the refinement registration step. Setting this to a 
-    smaller value excludes more frames."""
-
-    norm_frames: bool = True
-    """Determines whether to normalize frames during shift detection to improve registration accuracy."""
-
-    force_refImg: bool = False
-    """Determines whether to force the use of a pre-stored reference image for registration, instead of recomputing the 
-    image during runtime."""
-
-    pad_fft: bool = False
-    """Determines whether to pad the image during the FFT portion of the registration to reduce edge effects."""
-
-    do_regmetrics: bool = True
-    """Determines whether to compute the registration quality metrics. This step is optional, registration metrics are 
-    NOT used by the suite2p processing pipeline. However, these metrics are important for assessing the registration 
-    quality via the GUI. Note, computing the registration metrics is a fairly expensive operation, sometimes taking as 
-    much time as computing the registration offsets."""
-
-    reg_metric_n_pc: int = 10
-    """The number of Principle Components (PCs) used to compute the registration metrics. Note, the time to compute 
-    the registration metrics scales with the number of computed PCs, so it is recommended to keep the number as low 
-    as feasible for each use case."""
-
-
-@dataclass
-class OnePRegistration:
-    """Stores parameters for additional pre-registration processing used to improve the registration of 1-photon
-    datasets."""
-
-    one_p_reg: bool = False
-    """Determines whether to perform high-pass spatial filtering and tapering to improve one-photon image 
-    registration. For two-photon datasets, this should be set to False."""
-
-    spatial_hp_reg: int = 42
-    """The spatial high-pass filter window size, in pixels."""
-
-    pre_smooth: float = 0.0
-    """The standard deviation for Gaussian smoothing applied before spatial high-pass filtering. The smoothing will 
-    only be applied if this field is greater than 0.0."""
-
-    spatial_taper: float = 40.0
-    """The number of pixels to ignore at the image edges to reduce edge artifacts during registration."""
-
-
-@dataclass
-class NonRigid:
-    """Stores parameters for non-rigid registration, which is used to improve motion registration in complex
-    datasets by dividing frames into subregions and shifting each subregion independently of other subregions."""
-
-    nonrigid: bool = True
-    """Determines whether to perform non-rigid registration to correct for local motion and deformation. This is 
-    primarily used for correcting non-uniform motion."""
-
-    block_size: list[int] = field(default_factory=lambda: [128, 128])
-    """The block size, in pixels, for non-rigid registration, defining the dimensions of subregions used in 
-    the correction. It is recommended to keep this size a power of 2 and / or 3 for more efficient FFT computation. 
-    During processing, each frame will be split into sub-regions with these dimensions and the registration will then be
-    applied to each region."""
-
-    snr_thresh: float = 1.2
-    """The signal-to-noise ratio threshold. The phase correlation peak must be this many times higher than the 
-    noise level for the algorithm to accept the block shift and apply it to the output dataset."""
-
-    maxregshiftNR: float = 5.0
-    """The maximum allowed shift, in pixels, for each block relative to the rigid registration shift."""
-
-
-@dataclass
-class ROIDetection:
-    """Stores parameters for cell ROI detection."""
-
-    preclassify: float = 0.5
-    """The classifier probability threshold used to pre-filter the cells before signal extraction. This is the minimum 
-    classifier confidence value (that the classified ROI is a cell) for the ROI to be processed further. If this is set 
-    to 0.0, then all detected ROIs (cells) are kept."""
-
-    roidetect: bool = True
-    """Determines whether to perform ROI detection and classification."""
-
-    sparse_mode: bool = True
-    """Determines whether to use the sparse mode for cell detection, which is well-suited for data with sparse 
-    signals."""
-
-    spatial_scale: int = 0
-    """The optimal spatial scale, in pixels, for the processed data. This is used to adjust detection sensitivity. A 
-    value of 0 means automatic detection based on the data's spatial scale. Values above 0 are applied in increments of 
-    6 pixels (1 -> 6 pixels, 2-> 12 pixels, etc.)."""
-
-    connected: bool = True
-    """Determines whether to require the detected ROIs to be fully connected regions."""
-
-    threshold_scaling: float = 2.0
-    """The scaling factor for the detection threshold. This determines how distinctly ROIs have to stand out from 
-    background noise to be considered valid."""
-
-    spatial_hp_detect: int = 25
-    """The window size, in pixels, for spatial high-pass filtering applied before neuropil subtraction during 
-    ROI detection."""
-
-    max_overlap: float = 0.75
-    """The maximum allowed fraction of overlapping pixels between ROIs. ROIs that overlap above this threshold are be 
-    discarded."""
-
-    high_pass: int = 100
-    """The window size, in frames, for running mean subtraction over time to remove low-frequency ROI drift."""
-
-    smooth_masks: bool = True
-    """Determines whether to smooth the ROI masks in the final pass of cell detection."""
-
-    max_iterations: int = 50
-    """The maximum number of iterations allowed for cell extraction. Generally, more iterations lead to more accurate 
-    cell detection, but having the value too high may be detrimental."""
-
-    nbinned: int = 5000
-    """The maximum number of binned frames to use for ROI detection. Settings this value to a higher number leads to 
-    more ROIs being detected, but reduces processing speed and increases RAM overhead."""
-
-    denoise: bool = False
-    """Determines whether to denoise the binned movie before cell detection in sparse mode to enhance performance. 
-    If enabled, 'sparse_mode' has to be True."""
-
-
-@dataclass
-class CellposeDetection:
-    """Stores parameters for the Cellpose algorithm, which can optionally be used to improve cell ROI extraction."""
-
-    anatomical_only: int = 0
-    """Specifies the Cellpose mode for cell detection:
-        0: Do not use Cellpose. This automatically disables all other fields in this section.
-        1: Detect masks on the max projection divided by the mean image.
-        2: Detect masks on the mean image.
-        3: Detect masks on the enhanced mean image.
-        4: Detect masks on the max projection image.
-    """
-
-    diameter: int = 0
-    """Specifies the diameter, in pixels, to look for when finding cell ROIs. If set to 0, Cellpose estimates the 
-    diameter automatically.."""
-
-    cellprob_threshold: float = 0.0
-    """The threshold for cell detection, used to filter out low-confidence ROIs."""
-
-    flow_threshold: float = 1.5
-    """The flow threshold, used to control the algorithm's sensitivity to cell boundaries."""
-
-    spatial_hp_cp: int = 0
-    """The window size, in pixels, for spatial high-pass filtering applied to the image before Cellpose processing."""
-
-    pretrained_model: str = "cyto"
-    """Specifies the pretrained model to use for cell detection. Can be a built-in model name (e.g., 'cyto') or a 
-    path to a custom model."""
-
-
-@dataclass
-class SignalExtraction:
-    """Stores parameters for extracting fluorescence signals from ROIs and surrounding neuropil regions."""
-
-    neuropil_extract: bool = True
-    """Determines whether to extract neuropil signals. Typically, this is set to True to support later 
-    delta-fluorescence-over-fluorescence (dff) analysis."""
-
-    allow_overlap: bool = False
-    """Determines whether to allow overlap pixels (pixels shared by multiple ROIs) to be used in the signal extraction. 
-    Typically this is set to False to avoid contamination."""
-
-    min_neuropil_pixels: int = 350
-    """The minimum number of pixels required to compute the neuropil signal for each cell."""
-
-    inner_neuropil_radius: int = 2
-    """The number of pixels to keep between the ROI and the surrounding neuropil region to avoid signal bleed-over."""
-
-    lam_percentile: int = 50
-    """The percentile of Lambda within area to ignore when excluding the brightest pixels during neuropil extraction.
-    Specifically, pixels with relative brightness above this threshold are excluded from neuropil signal to filter 
-    out bright speckle outliers.
-    """
-
-
-@dataclass
-class SpikeDeconvolution:
-    """Stores parameters for deconvolve fluorescence signals to infer spike trains."""
-
-    spikedetect: bool = True
-    """Determines whether to perform fluorescence spike deconvolution."""
-
-    neucoeff: float = 0.7
-    """The neuropil coefficient applied for signal correction before deconvolution. Specifically, the neuropil signal
-    is scaled by this coefficient before it is subtracted from the ROI signal when computing df/f values."""
-
-    baseline: str = "maximin"
-    """Specifies the method to compute the baseline of each trace. This baseline is then subtracted from each cell's 
-    fluorescence. ‘maximin’ computes a moving baseline by filtering the data with a Gaussian of width 
-    'sig_baseline' * 'fs', and then minimum filtering with a window of 'win_baseline' * 'fs', and then maximum 
-    filtering with the same window. ‘constant’ computes a constant baseline by filtering with a Gaussian of width 
-    'sig_baseline' * 'fs' and then taking the minimum value of this filtered trace. ‘constant_percentile’ computes a 
-    constant baseline by taking the 'prctile_baseline' percentile of the trace."""
-
-    win_baseline: float = 60.0
-    """The time window, in seconds, over which to compute the baseline filter."""
-
-    sig_baseline: float = 10.0
-    """The standard deviation, in seconds, of the Gaussian filter applied to smooth the baseline signal."""
-
-    prctile_baseline: float = 8.0
-    """The percentile used to determine the baseline level of each trace (typically a low percentile reflecting 
-    minimal activity)."""
-
-
-@dataclass
-class Classification:
-    """Stores parameters for classifying detected ROIs as real cells or artifacts."""
-
-    soma_crop: bool = True
-    """Determines whether to crop dendritic regions from detected ROIs to focus on the cell body for classification 
-    purposes."""
-
-    use_builtin_classifier: bool = False
-    """Determines whether to use the built-in classifier for cell detection."""
-
-    classifier_path: str = ""
-    """The path to a custom classifier file, if not using the built-in classifier."""
-
-
-@dataclass
-class Channel2:
-    """Stores parameters for processing the second channel in multichannel datasets."""
-
-    chan2_thres: float = 0.65
-    """The threshold for considering an ROI detected in one channel as detected (present) in the second channel. 
-    This threshold specifies the ratio of channel 1 pixels to channel 2 pixels for the ROI to be considered present in 
-    both channels."""
-
-
-@dataclass
-class SingleDayS2PConfiguration(YamlConfig):
-    """Aggregates all user-addressable parameters of the single-day suite2p pipeline used to discover cell ROIs and
-    extract their fluorescence data.
-
-    This class is used during single-day processing to instruct suite2p on how to process the data. This class is based
-    on the 'default_ops' from the original suite2p package. As part of the suite2p refactoring performed in sl-suite2p
-    package, the 'default_ops' has been replaced with this class instance. Compared to the 'original' ops, it allows
-    saving configuration parameters as a .YAML file, which offers a better way of viewing and editing the parameters and
-    running suite2p pipeline on remote compute servers.
-    """
-
-    # Define the instances of each nested settings class as fields
-    main: Main = field(default_factory=Main)
-    """Stores global parameters that broadly define the suite2p single-day processing configuration."""
-    file_io: FileIO = field(default_factory=FileIO)
-    """Stores general I/O parameters that specify input data location, format, and working and output directories."""
-    output: Output = field(default_factory=Output)
-    """Stores parameters for aggregating and saving the processing results of each plane as a unified directory or
-    file."""
-    registration: Registration = field(default_factory=Registration)
-    """Stores parameters for rigid registration, which is used to correct motion artifacts between frames by
-    counter-shifting the entire frame."""
-    one_p_registration: OnePRegistration = field(default_factory=OnePRegistration)
-    """Stores parameters for additional pre-registration processing used to improve the registration of 1-photon
-    datasets."""
-    non_rigid: NonRigid = field(default_factory=NonRigid)
-    """Stores parameters for non-rigid registration, which is used to improve motion registration in complex 
-    datasets."""
-    roi_detection: ROIDetection = field(default_factory=ROIDetection)
-    """Stores parameters for cell ROI detection and extraction."""
-    cellpose_detection: CellposeDetection = field(default_factory=CellposeDetection)
-    """Stores parameters for the Cellpose algorithm, which can optionally be used to improve cell ROI extraction."""
-    signal_extraction: SignalExtraction = field(default_factory=SignalExtraction)
-    """Stores parameters for extracting fluorescence signals from ROIs and surrounding neuropil regions."""
-    spike_deconvolution: SpikeDeconvolution = field(default_factory=SpikeDeconvolution)
-    """Stores parameters for deconvolve fluorescence signals to infer spike trains."""
-    classification: Classification = field(default_factory=Classification)
-    """Stores parameters for classifying detected ROIs as real cells or artifacts."""
-    channel2: Channel2 = field(default_factory=Channel2)
-    """Stores parameters for processing the second channel in multichannel datasets."""
-
-    def to_npy(self, output_directory: Path) -> None:
-        """Saves the managed configuration data as an 'ops.npy' file under the target directory.
-
-        This method is mostly called by internal sl-suite2p functions to translate the user-specified configuration
-        file into the format used by suite2p pipelines.
-
-        Notes:
-            If the target output directory does not exist when this method is called, it will be created.
-
-        Args:
-            output_directory: The path to the directory where the 'ops.npy' file should be saved.
-        """
-        ensure_directory_exists(output_directory)  # Creates the directory, if necessary
-        file_path = output_directory.joinpath("ops.npy")  # Computes the output path
-        np.save(file_path, self.to_ops(), allow_pickle=True)  # Dumps the configuration data to 'ops.npy' file.
-
-    def to_config(self, output_directory: Path) -> None:
-        """Saves the managed configuration data as a 'single_day_s2p_configuration.yaml' file under the target
-        directory.
-
-        This method is typically used to dump the 'default' configuration parameters to disk as a user-editable
-        .yaml file. The user is then expected to modify these parameters as needed, before the class data is loaded and
-        used by the suite2p pipeline.
-
-        Notes:
-            If the target output directory does not exist when this method is called, it will be created.
-
-        Args:
-            output_directory: The path to the directory where the 'single_day_s2p_configuration.yaml' file should be
-            saved.
-        """
-        ensure_directory_exists(output_directory)  # Creates the directory, if necessary
-        file_path = output_directory.joinpath("single_day_s2p_configuration.yaml")   # Computes the output path
-
-        # Note, this uses the same configuration name as the SessionData class, making it automatically compatible with
-        # Sun lab data structure.
-        self.to_yaml(file_path=file_path)  # Dumps the data to a 'yaml' file.
-
-    def to_ops(self) -> dict[str, Any]:
-        """Converts the class instance to a dictionary and returns it to caller.
-
-        This method is mostly called by internal sl-suite2p functions to translate the default configuration parameters
-        to the dictionary format used by suite2p pipelines.
-        """
-
-        # Creates an empty dictionary to store all keys and values
-        combined_ops = {}
-
-        # Iterates through all dataclass fields
-        # noinspection PyTypeChecker
-        for section_name, section in asdict(self).items():
-            # Adds all keys and values from each section to the combined dictionary
-            if isinstance(section, dict):
-                combined_ops.update(section)
-
-        return combined_ops

sl_shared_assets-1.0.0rc19.dist-info/RECORD

@@ -1,23 +0,0 @@
-sl_shared_assets/__init__.py,sha256=VASYVzsHnaFykp1xdEjOgQdnfuqwokaKIp387zXyFqA,2080
-sl_shared_assets/cli.py,sha256=a4Ja2gm4ykOac7QmHen14Jhgu6955IUQDZrysp1RpFM,4207
-sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sl_shared_assets/data_classes/__init__.py,sha256=pq-iyd4eyv1CPVcLcQQJBVAm7XCDWuZqxurrLOMW3e0,1702
-sl_shared_assets/data_classes/configuration_data.py,sha256=zKZ3cE2pZFDRiQ7off8hu2nV9JsBly9Phc5goY4qCH4,4163
-sl_shared_assets/data_classes/runtime_data.py,sha256=jSCvZG01gkcSUexFiKITjTJ8ZoF18qRfxiwhyrWW7-I,13964
-sl_shared_assets/data_classes/session_data.py,sha256=sRHgHNR4x1hc0dKLVteyz2tmYJrF2pKP9wzoqG1lxTg,81866
-sl_shared_assets/data_classes/surgery_data.py,sha256=Z4QZAZCz0_w7qrGMMzYn-fwwwycw3ki9SPJU0kD5Ap4,7425
-sl_shared_assets/server/__init__.py,sha256=nyX6-9ACcrQeRQOCNvBVrWSTHGjRPANIG_u0aq7HPTg,426
-sl_shared_assets/server/job.py,sha256=M7ZytqhluEV-YQPM9VQV3SqK-F9egQ3UcLc1SLBH4rA,7885
-sl_shared_assets/server/server.py,sha256=NpqWVjvxdtxHZIooBVaKY2jEBDN3dGohBzrFA0TSKIU,9380
-sl_shared_assets/suite2p/__init__.py,sha256=8N2BQNINBkH7JNODmYACHhvUH_uurTuw7w0PW3rVRYM,411
-sl_shared_assets/suite2p/multi_day.py,sha256=2_AHI91wuxwS07GFJn8S1454uLrQGmt0bS_qBoZsHVc,13102
-sl_shared_assets/suite2p/single_day.py,sha256=7dgYN9FnIvxNL0uHo0CtoLng2nRxZJYtV_AfskMt6tE,29961
-sl_shared_assets/tools/__init__.py,sha256=UWrNfseGupOrY4OK2PgDEJ-Q3LbSrPLC2pfaLm8wYBA,468
-sl_shared_assets/tools/ascension_tools.py,sha256=y2w72Czpbw9LwgsbdEx_ckzMKTZ78cgKPTIk6vRYmAk,15877
-sl_shared_assets/tools/packaging_tools.py,sha256=LOKCKvT6UD_cidCONaI4ctWyej5zEwwdhhgwYrj60Kg,6746
-sl_shared_assets/tools/transfer_tools.py,sha256=J26kwOp_NpPSY0-xu5FTw9udte-rm_mW1FJyaTNoqQI,6606
-sl_shared_assets-1.0.0rc19.dist-info/METADATA,sha256=7V58TU4cUqBvoc6f9az3PuPSj46D11UYHQ_mC_lBsNU,47884
-sl_shared_assets-1.0.0rc19.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-sl_shared_assets-1.0.0rc19.dist-info/entry_points.txt,sha256=bdnmVAcK3nrKi9QEYeNMrCLFH5LQ4BMBfwbLIgLPtq4,222
-sl_shared_assets-1.0.0rc19.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-1.0.0rc19.dist-info/RECORD,,

sl_shared_assets-1.0.0rc19.dist-info/entry_points.txt

@@ -1,4 +0,0 @@
-[console_scripts]
-sl-ascend = sl_shared_assets.cli:ascend_tyche_directory
-sl-generate-credentials = sl_shared_assets.cli:generate_server_credentials_file
-sl-replace-root = sl_shared_assets.cli:replace_local_root_directory